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<FONT color="green">001</FONT>    package edu.hawaii.myisern.model;<a name="line.1"></a>
<FONT color="green">002</FONT>    <a name="line.2"></a>
<FONT color="green">003</FONT>    import java.math.BigInteger;<a name="line.3"></a>
<FONT color="green">004</FONT>    import java.util.ArrayList;<a name="line.4"></a>
<FONT color="green">005</FONT>    import java.util.List;<a name="line.5"></a>
<FONT color="green">006</FONT>    import java.util.Map;<a name="line.6"></a>
<FONT color="green">007</FONT>    import java.util.TreeMap;<a name="line.7"></a>
<FONT color="green">008</FONT>    import edu.hawaii.myisern.collaborations.jaxb.Collaboration;<a name="line.8"></a>
<FONT color="green">009</FONT>    import edu.hawaii.myisern.organizations.jaxb.Organization;<a name="line.9"></a>
<FONT color="green">010</FONT>    import edu.hawaii.myisern.researchers.jaxb.Researcher;<a name="line.10"></a>
<FONT color="green">011</FONT>    <a name="line.11"></a>
<FONT color="green">012</FONT>    /**<a name="line.12"></a>
<FONT color="green">013</FONT>     * Performs semantic checks on lists of Collaboration, Researcher, and Organization data.<a name="line.13"></a>
<FONT color="green">014</FONT>     * <a name="line.14"></a>
<FONT color="green">015</FONT>     * @author Andrew Wong, Laura Matsuo<a name="line.15"></a>
<FONT color="green">016</FONT>     *<a name="line.16"></a>
<FONT color="green">017</FONT>     */<a name="line.17"></a>
<FONT color="green">018</FONT>    public class XmlSemanticChecker {<a name="line.18"></a>
<FONT color="green">019</FONT>      private List&lt;Collaboration&gt; collaborationList;<a name="line.19"></a>
<FONT color="green">020</FONT>      private List&lt;Researcher&gt; researcherList;<a name="line.20"></a>
<FONT color="green">021</FONT>      private List&lt;Organization&gt; organizationList;<a name="line.21"></a>
<FONT color="green">022</FONT>    <a name="line.22"></a>
<FONT color="green">023</FONT>      private List&lt;String&gt; errorList;<a name="line.23"></a>
<FONT color="green">024</FONT>      <a name="line.24"></a>
<FONT color="green">025</FONT>      boolean verboseMode;<a name="line.25"></a>
<FONT color="green">026</FONT>    <a name="line.26"></a>
<FONT color="green">027</FONT>      /**<a name="line.27"></a>
<FONT color="green">028</FONT>       * Sets mode of operation.  &lt;p&gt;<a name="line.28"></a>
<FONT color="green">029</FONT>       * false = all invalid entries are removed&lt;br&gt;<a name="line.29"></a>
<FONT color="green">030</FONT>       * true = no entries are removed, but warning messages are shown<a name="line.30"></a>
<FONT color="green">031</FONT>       * <a name="line.31"></a>
<FONT color="green">032</FONT>       * @param newMode Mode of operation.<a name="line.32"></a>
<FONT color="green">033</FONT>       */<a name="line.33"></a>
<FONT color="green">034</FONT>      public void setMode(boolean newMode) {<a name="line.34"></a>
<FONT color="green">035</FONT>        verboseMode = newMode;<a name="line.35"></a>
<FONT color="green">036</FONT>      }<a name="line.36"></a>
<FONT color="green">037</FONT>      <a name="line.37"></a>
<FONT color="green">038</FONT>      /**<a name="line.38"></a>
<FONT color="green">039</FONT>       * Listing of UniqueID types.<a name="line.39"></a>
<FONT color="green">040</FONT>       */<a name="line.40"></a>
<FONT color="green">041</FONT>      enum idType { idCollaboration, idResearcher, idOrganization };<a name="line.41"></a>
<FONT color="green">042</FONT>      <a name="line.42"></a>
<FONT color="green">043</FONT>      /**<a name="line.43"></a>
<FONT color="green">044</FONT>       * Constructor.  Initializes list of id values.<a name="line.44"></a>
<FONT color="green">045</FONT>       */<a name="line.45"></a>
<FONT color="green">046</FONT>      public XmlSemanticChecker () {<a name="line.46"></a>
<FONT color="green">047</FONT>        uniqueIdList = new TreeMap&lt;String, idType&gt;();<a name="line.47"></a>
<FONT color="green">048</FONT>        verboseMode = true;<a name="line.48"></a>
<FONT color="green">049</FONT>        <a name="line.49"></a>
<FONT color="green">050</FONT>        errorList = new ArrayList&lt;String&gt;();<a name="line.50"></a>
<FONT color="green">051</FONT>      }<a name="line.51"></a>
<FONT color="green">052</FONT>      <a name="line.52"></a>
<FONT color="green">053</FONT>      /**<a name="line.53"></a>
<FONT color="green">054</FONT>       * Sets the collaboration list that is checked.<a name="line.54"></a>
<FONT color="green">055</FONT>       * <a name="line.55"></a>
<FONT color="green">056</FONT>       * @param list New collaboration list.<a name="line.56"></a>
<FONT color="green">057</FONT>       */<a name="line.57"></a>
<FONT color="green">058</FONT>      public void setCollaborationList(List&lt;Collaboration&gt; list) {<a name="line.58"></a>
<FONT color="green">059</FONT>        collaborationList = list;<a name="line.59"></a>
<FONT color="green">060</FONT>      }<a name="line.60"></a>
<FONT color="green">061</FONT>    <a name="line.61"></a>
<FONT color="green">062</FONT>      /**<a name="line.62"></a>
<FONT color="green">063</FONT>       * Sets the researcher list that is checked.<a name="line.63"></a>
<FONT color="green">064</FONT>       * <a name="line.64"></a>
<FONT color="green">065</FONT>       * @param list New researcher list.<a name="line.65"></a>
<FONT color="green">066</FONT>       */<a name="line.66"></a>
<FONT color="green">067</FONT>      public void setResearcherList(List&lt;Researcher&gt; list) {<a name="line.67"></a>
<FONT color="green">068</FONT>        researcherList = list;<a name="line.68"></a>
<FONT color="green">069</FONT>      }<a name="line.69"></a>
<FONT color="green">070</FONT>    <a name="line.70"></a>
<FONT color="green">071</FONT>      /**<a name="line.71"></a>
<FONT color="green">072</FONT>       * Sets the organization list that is checked.<a name="line.72"></a>
<FONT color="green">073</FONT>       * <a name="line.73"></a>
<FONT color="green">074</FONT>       * @param list New organization list.<a name="line.74"></a>
<FONT color="green">075</FONT>       */<a name="line.75"></a>
<FONT color="green">076</FONT>      public void setOrganizationList(List&lt;Organization&gt; list) {<a name="line.76"></a>
<FONT color="green">077</FONT>        organizationList = list;<a name="line.77"></a>
<FONT color="green">078</FONT>      }<a name="line.78"></a>
<FONT color="green">079</FONT>    <a name="line.79"></a>
<FONT color="green">080</FONT>      /**<a name="line.80"></a>
<FONT color="green">081</FONT>       * Retrieves the Collaboration list.<a name="line.81"></a>
<FONT color="green">082</FONT>       * <a name="line.82"></a>
<FONT color="green">083</FONT>       * @return List of collaborations.<a name="line.83"></a>
<FONT color="green">084</FONT>       */<a name="line.84"></a>
<FONT color="green">085</FONT>      public List&lt;Collaboration&gt; getCollaborationList() {<a name="line.85"></a>
<FONT color="green">086</FONT>        return collaborationList;<a name="line.86"></a>
<FONT color="green">087</FONT>      }<a name="line.87"></a>
<FONT color="green">088</FONT>    <a name="line.88"></a>
<FONT color="green">089</FONT>      /**<a name="line.89"></a>
<FONT color="green">090</FONT>       * Retrieves the Organization list.<a name="line.90"></a>
<FONT color="green">091</FONT>       * <a name="line.91"></a>
<FONT color="green">092</FONT>       * @return List of organizations.<a name="line.92"></a>
<FONT color="green">093</FONT>       */<a name="line.93"></a>
<FONT color="green">094</FONT>      public List&lt;Organization&gt; getOrganizationList() {<a name="line.94"></a>
<FONT color="green">095</FONT>        return organizationList;<a name="line.95"></a>
<FONT color="green">096</FONT>      }<a name="line.96"></a>
<FONT color="green">097</FONT>    <a name="line.97"></a>
<FONT color="green">098</FONT>      /**<a name="line.98"></a>
<FONT color="green">099</FONT>       * Retrieves the Researcher list.<a name="line.99"></a>
<FONT color="green">100</FONT>       * <a name="line.100"></a>
<FONT color="green">101</FONT>       * @return List of researchers.<a name="line.101"></a>
<FONT color="green">102</FONT>       */<a name="line.102"></a>
<FONT color="green">103</FONT>      public List&lt;Researcher&gt; getResearcherList() {<a name="line.103"></a>
<FONT color="green">104</FONT>        return researcherList;<a name="line.104"></a>
<FONT color="green">105</FONT>      }<a name="line.105"></a>
<FONT color="green">106</FONT>    <a name="line.106"></a>
<FONT color="green">107</FONT>      Map&lt;String, idType&gt; uniqueIdList;  <a name="line.107"></a>
<FONT color="green">108</FONT>      <a name="line.108"></a>
<FONT color="green">109</FONT>      /**<a name="line.109"></a>
<FONT color="green">110</FONT>       * Checks if a given unique ID exists.<a name="line.110"></a>
<FONT color="green">111</FONT>       * <a name="line.111"></a>
<FONT color="green">112</FONT>       * @param id Unique ID to look up<a name="line.112"></a>
<FONT color="green">113</FONT>       * @param type Type of unique ID.<a name="line.113"></a>
<FONT color="green">114</FONT>       * @return true if an object with UniqueID id exists, false if not.<a name="line.114"></a>
<FONT color="green">115</FONT>       */<a name="line.115"></a>
<FONT color="green">116</FONT>      private boolean checkUniqueId(String id, idType type) {<a name="line.116"></a>
<FONT color="green">117</FONT>        if (id == null) {<a name="line.117"></a>
<FONT color="green">118</FONT>          // we return true here since we may have a researcher with no organization<a name="line.118"></a>
<FONT color="green">119</FONT>          // or something similar<a name="line.119"></a>
<FONT color="green">120</FONT>          return true;<a name="line.120"></a>
<FONT color="green">121</FONT>        }<a name="line.121"></a>
<FONT color="green">122</FONT>        <a name="line.122"></a>
<FONT color="green">123</FONT>        String val = id.replace(' ', '_');<a name="line.123"></a>
<FONT color="green">124</FONT>    <a name="line.124"></a>
<FONT color="green">125</FONT>        if (this.uniqueIdList.containsKey(val) &amp;&amp;<a name="line.125"></a>
<FONT color="green">126</FONT>            this.uniqueIdList.get(val) == type) {<a name="line.126"></a>
<FONT color="green">127</FONT>          return true;<a name="line.127"></a>
<FONT color="green">128</FONT>        }<a name="line.128"></a>
<FONT color="green">129</FONT>    <a name="line.129"></a>
<FONT color="green">130</FONT>        return false;<a name="line.130"></a>
<FONT color="green">131</FONT>      }<a name="line.131"></a>
<FONT color="green">132</FONT>      <a name="line.132"></a>
<FONT color="green">133</FONT>      /**<a name="line.133"></a>
<FONT color="green">134</FONT>       * Checks if given id exists, and if not, adds it to the list.<a name="line.134"></a>
<FONT color="green">135</FONT>       * <a name="line.135"></a>
<FONT color="green">136</FONT>       * @param id ID value.  Spaces are converted to underscores.<a name="line.136"></a>
<FONT color="green">137</FONT>       * @param type Type of unique ID.<a name="line.137"></a>
<FONT color="green">138</FONT>       * @return false if id already exists, true if not.  If true is returned, id is<a name="line.138"></a>
<FONT color="green">139</FONT>       *         added to list, so a later call would return false.<a name="line.139"></a>
<FONT color="green">140</FONT>       */<a name="line.140"></a>
<FONT color="green">141</FONT>      private boolean addUniqueId(String id, idType type) {<a name="line.141"></a>
<FONT color="green">142</FONT>        // ensure id is not empty (either null string or empty string)<a name="line.142"></a>
<FONT color="green">143</FONT>        if (id == null || id == "") {<a name="line.143"></a>
<FONT color="green">144</FONT>          return false;<a name="line.144"></a>
<FONT color="green">145</FONT>        }<a name="line.145"></a>
<FONT color="green">146</FONT>        <a name="line.146"></a>
<FONT color="green">147</FONT>        String val = id.replace(' ', '_');<a name="line.147"></a>
<FONT color="green">148</FONT>        <a name="line.148"></a>
<FONT color="green">149</FONT>        if (this.uniqueIdList.containsKey(val)) {<a name="line.149"></a>
<FONT color="green">150</FONT>          // already in set, thus isn't a valid ID<a name="line.150"></a>
<FONT color="green">151</FONT>          return false;<a name="line.151"></a>
<FONT color="green">152</FONT>        }<a name="line.152"></a>
<FONT color="green">153</FONT>    <a name="line.153"></a>
<FONT color="green">154</FONT>        this.uniqueIdList.put(val, type);<a name="line.154"></a>
<FONT color="green">155</FONT>        return true;<a name="line.155"></a>
<FONT color="green">156</FONT>      }<a name="line.156"></a>
<FONT color="green">157</FONT>      <a name="line.157"></a>
<FONT color="green">158</FONT>      /**<a name="line.158"></a>
<FONT color="green">159</FONT>       * Outputs string if verboseMode is set.<a name="line.159"></a>
<FONT color="green">160</FONT>       * <a name="line.160"></a>
<FONT color="green">161</FONT>       * @param info String to write to screen.<a name="line.161"></a>
<FONT color="green">162</FONT>       */<a name="line.162"></a>
<FONT color="green">163</FONT>      private void outputInfo(String info) {<a name="line.163"></a>
<FONT color="green">164</FONT>        if (this.verboseMode) {<a name="line.164"></a>
<FONT color="green">165</FONT>    //      System.out.println(info);<a name="line.165"></a>
<FONT color="green">166</FONT>          errorList.add(info);<a name="line.166"></a>
<FONT color="green">167</FONT>        }<a name="line.167"></a>
<FONT color="green">168</FONT>      }<a name="line.168"></a>
<FONT color="green">169</FONT>      <a name="line.169"></a>
<FONT color="green">170</FONT>      /**<a name="line.170"></a>
<FONT color="green">171</FONT>       * Checks if the specified Researcher object is valid.<a name="line.171"></a>
<FONT color="green">172</FONT>       * <a name="line.172"></a>
<FONT color="green">173</FONT>       * @param item Researcher in question<a name="line.173"></a>
<FONT color="green">174</FONT>       * @return true if it is a valid Researcher, false otherwise<a name="line.174"></a>
<FONT color="green">175</FONT>       */<a name="line.175"></a>
<FONT color="green">176</FONT>      private boolean validResearcher(Researcher item) {<a name="line.176"></a>
<FONT color="green">177</FONT>        <a name="line.177"></a>
<FONT color="green">178</FONT>        if (item.getUniqueID() != null) {<a name="line.178"></a>
<FONT color="green">179</FONT>          // UniqueID is already set, so it was already checked<a name="line.179"></a>
<FONT color="green">180</FONT>          this.uniqueIdList.put(item.getUniqueID(), idType.idResearcher);<a name="line.180"></a>
<FONT color="green">181</FONT>          return true;<a name="line.181"></a>
<FONT color="green">182</FONT>        }<a name="line.182"></a>
<FONT color="green">183</FONT>    <a name="line.183"></a>
<FONT color="green">184</FONT>        if (!this.addUniqueId(item.getName(), idType.idResearcher ) ) {<a name="line.184"></a>
<FONT color="green">185</FONT>          // ID is a duplicate<a name="line.185"></a>
<FONT color="green">186</FONT>          outputInfo("RESEARCHER ID CONFLICT: " + item.getName() );<a name="line.186"></a>
<FONT color="green">187</FONT>          return false;<a name="line.187"></a>
<FONT color="green">188</FONT>        }<a name="line.188"></a>
<FONT color="green">189</FONT>        <a name="line.189"></a>
<FONT color="green">190</FONT>        return true;<a name="line.190"></a>
<FONT color="green">191</FONT>      }<a name="line.191"></a>
<FONT color="green">192</FONT>      <a name="line.192"></a>
<FONT color="green">193</FONT>      /**<a name="line.193"></a>
<FONT color="green">194</FONT>       * Checks if the specified Collaboration object is valid.<a name="line.194"></a>
<FONT color="green">195</FONT>       * <a name="line.195"></a>
<FONT color="green">196</FONT>       * @param item Collaboration in question<a name="line.196"></a>
<FONT color="green">197</FONT>       * @return true if it is a valid Collaboration, false otherwise<a name="line.197"></a>
<FONT color="green">198</FONT>       */<a name="line.198"></a>
<FONT color="green">199</FONT>      private boolean validCollaboration(Collaboration item) {<a name="line.199"></a>
<FONT color="green">200</FONT>    <a name="line.200"></a>
<FONT color="green">201</FONT>        BigInteger LOWER_YEAR = new BigInteger("1990");<a name="line.201"></a>
<FONT color="green">202</FONT>        BigInteger UPPER_YEAR = new BigInteger("2010");<a name="line.202"></a>
<FONT color="green">203</FONT>        <a name="line.203"></a>
<FONT color="green">204</FONT>        if (item.getUniqueID() != null) {<a name="line.204"></a>
<FONT color="green">205</FONT>          // UniqueID is already set, so it was already checked<a name="line.205"></a>
<FONT color="green">206</FONT>          this.uniqueIdList.put(item.getUniqueID(), idType.idCollaboration);<a name="line.206"></a>
<FONT color="green">207</FONT>          return true;<a name="line.207"></a>
<FONT color="green">208</FONT>        }<a name="line.208"></a>
<FONT color="green">209</FONT>        <a name="line.209"></a>
<FONT color="green">210</FONT>        if (item.getYears() != null) {<a name="line.210"></a>
<FONT color="green">211</FONT>          for (BigInteger year : item.getYears().getYear() ) {<a name="line.211"></a>
<FONT color="green">212</FONT>            if (year.compareTo(LOWER_YEAR) == -1 ) {<a name="line.212"></a>
<FONT color="green">213</FONT>              outputInfo(item.getName() + ": invalid year " + year.toString() <a name="line.213"></a>
<FONT color="green">214</FONT>                  + " is less than " + LOWER_YEAR);<a name="line.214"></a>
<FONT color="green">215</FONT>              return false;<a name="line.215"></a>
<FONT color="green">216</FONT>            }<a name="line.216"></a>
<FONT color="green">217</FONT>            if (year.compareTo(UPPER_YEAR) == 1 ) {<a name="line.217"></a>
<FONT color="green">218</FONT>              outputInfo(item.getName() + ": invalid year " + year.toString() <a name="line.218"></a>
<FONT color="green">219</FONT>                  + " is greater than " + LOWER_YEAR);<a name="line.219"></a>
<FONT color="green">220</FONT>              return false;<a name="line.220"></a>
<FONT color="green">221</FONT>            }<a name="line.221"></a>
<FONT color="green">222</FONT>          }<a name="line.222"></a>
<FONT color="green">223</FONT>        }<a name="line.223"></a>
<FONT color="green">224</FONT>        <a name="line.224"></a>
<FONT color="green">225</FONT>        if (!this.addUniqueId(item.getName(), idType.idCollaboration ) ) {<a name="line.225"></a>
<FONT color="green">226</FONT>          // ID is a duplicate<a name="line.226"></a>
<FONT color="green">227</FONT>          outputInfo("COLLABORATION ID CONFLICT: " + item.getName() );<a name="line.227"></a>
<FONT color="green">228</FONT>          return false;<a name="line.228"></a>
<FONT color="green">229</FONT>        }<a name="line.229"></a>
<FONT color="green">230</FONT>        <a name="line.230"></a>
<FONT color="green">231</FONT>        return true;<a name="line.231"></a>
<FONT color="green">232</FONT>      }<a name="line.232"></a>
<FONT color="green">233</FONT>      <a name="line.233"></a>
<FONT color="green">234</FONT>      /**<a name="line.234"></a>
<FONT color="green">235</FONT>       * Checks if the specified Organization object is valid.<a name="line.235"></a>
<FONT color="green">236</FONT>       * <a name="line.236"></a>
<FONT color="green">237</FONT>       * @param item Organization in question<a name="line.237"></a>
<FONT color="green">238</FONT>       * @return true if it is a valid Organization, false otherwise<a name="line.238"></a>
<FONT color="green">239</FONT>       */<a name="line.239"></a>
<FONT color="green">240</FONT>      private boolean validOrganization(Organization item) {<a name="line.240"></a>
<FONT color="green">241</FONT>    <a name="line.241"></a>
<FONT color="green">242</FONT>        if (item.getUniqueID() != null) {<a name="line.242"></a>
<FONT color="green">243</FONT>          // UniqueID is already set, so it was already checked<a name="line.243"></a>
<FONT color="green">244</FONT>          this.uniqueIdList.put(item.getUniqueID(), idType.idOrganization);<a name="line.244"></a>
<FONT color="green">245</FONT>          return true;<a name="line.245"></a>
<FONT color="green">246</FONT>        }<a name="line.246"></a>
<FONT color="green">247</FONT>        <a name="line.247"></a>
<FONT color="green">248</FONT>        if (!this.addUniqueId(item.getName(), idType.idOrganization ) ) {<a name="line.248"></a>
<FONT color="green">249</FONT>          // ID is a duplicate<a name="line.249"></a>
<FONT color="green">250</FONT>          outputInfo("ORGANIZATION ID CONFLICT: " + item.getName() );<a name="line.250"></a>
<FONT color="green">251</FONT>          return false;<a name="line.251"></a>
<FONT color="green">252</FONT>        }<a name="line.252"></a>
<FONT color="green">253</FONT>        <a name="line.253"></a>
<FONT color="green">254</FONT>        return true;<a name="line.254"></a>
<FONT color="green">255</FONT>      }<a name="line.255"></a>
<FONT color="green">256</FONT>      <a name="line.256"></a>
<FONT color="green">257</FONT>      /**<a name="line.257"></a>
<FONT color="green">258</FONT>       * Checks researchers list and removes invalid entries.<a name="line.258"></a>
<FONT color="green">259</FONT>       * <a name="line.259"></a>
<FONT color="green">260</FONT>       * @return Number of entries in all lists that failed semantic checks.<a name="line.260"></a>
<FONT color="green">261</FONT>       */<a name="line.261"></a>
<FONT color="green">262</FONT>      public int checkResearchers() {<a name="line.262"></a>
<FONT color="green">263</FONT>        int count = 0;<a name="line.263"></a>
<FONT color="green">264</FONT>        <a name="line.264"></a>
<FONT color="green">265</FONT>        List&lt;Researcher&gt; result = new ArrayList&lt;Researcher&gt;();<a name="line.265"></a>
<FONT color="green">266</FONT>        <a name="line.266"></a>
<FONT color="green">267</FONT>        for (Researcher item : this.researcherList) {<a name="line.267"></a>
<FONT color="green">268</FONT>          if (validResearcher(item)) {<a name="line.268"></a>
<FONT color="green">269</FONT>            item.setUniqueID(item.getName().replace(' ', '_'));<a name="line.269"></a>
<FONT color="green">270</FONT>            result.add(item);<a name="line.270"></a>
<FONT color="green">271</FONT>          }<a name="line.271"></a>
<FONT color="green">272</FONT>          else {<a name="line.272"></a>
<FONT color="green">273</FONT>            count++;<a name="line.273"></a>
<FONT color="green">274</FONT>          }<a name="line.274"></a>
<FONT color="green">275</FONT>        }<a name="line.275"></a>
<FONT color="green">276</FONT>    <a name="line.276"></a>
<FONT color="green">277</FONT>        if (!verboseMode) {<a name="line.277"></a>
<FONT color="green">278</FONT>          researcherList = result;<a name="line.278"></a>
<FONT color="green">279</FONT>        }<a name="line.279"></a>
<FONT color="green">280</FONT>        <a name="line.280"></a>
<FONT color="green">281</FONT>        return count;<a name="line.281"></a>
<FONT color="green">282</FONT>      }<a name="line.282"></a>
<FONT color="green">283</FONT>     <a name="line.283"></a>
<FONT color="green">284</FONT>      /**<a name="line.284"></a>
<FONT color="green">285</FONT>       * Checks that the links in each list are valid.  This function should not<a name="line.285"></a>
<FONT color="green">286</FONT>       * be called until all three lists are processed, since there is no way to<a name="line.286"></a>
<FONT color="green">287</FONT>       * check links in one pass.<a name="line.287"></a>
<FONT color="green">288</FONT>       * <a name="line.288"></a>
<FONT color="green">289</FONT>       * @return Number of entries that are removed<a name="line.289"></a>
<FONT color="green">290</FONT>       */<a name="line.290"></a>
<FONT color="green">291</FONT>      public int checkLinks() {<a name="line.291"></a>
<FONT color="green">292</FONT>        List&lt;Collaboration&gt; cResult = new ArrayList&lt;Collaboration&gt;();<a name="line.292"></a>
<FONT color="green">293</FONT>        List&lt;Organization&gt;  oResult = new ArrayList&lt;Organization&gt;();<a name="line.293"></a>
<FONT color="green">294</FONT>        List&lt;Researcher&gt;    rResult = new ArrayList&lt;Researcher&gt;();<a name="line.294"></a>
<FONT color="green">295</FONT>        <a name="line.295"></a>
<FONT color="green">296</FONT>        int count = 0;<a name="line.296"></a>
<FONT color="green">297</FONT>        boolean valid;<a name="line.297"></a>
<FONT color="green">298</FONT>        for (Collaboration item : this.collaborationList) {<a name="line.298"></a>
<FONT color="green">299</FONT>          valid = true;<a name="line.299"></a>
<FONT color="green">300</FONT>      <a name="line.300"></a>
<FONT color="green">301</FONT>          for (String link : item.getCollaboratingOrganizations().getCollaboratingOrganization()) {<a name="line.301"></a>
<FONT color="green">302</FONT>            boolean validLink = this.checkUniqueId(link, idType.idOrganization);<a name="line.302"></a>
<FONT color="green">303</FONT>            if (!validLink) {<a name="line.303"></a>
<FONT color="green">304</FONT>              outputInfo("Collaboration " + item.getName() + ": Invalid organization: " + link);<a name="line.304"></a>
<FONT color="green">305</FONT>            }<a name="line.305"></a>
<FONT color="green">306</FONT>            <a name="line.306"></a>
<FONT color="green">307</FONT>            valid = valid &amp; validLink;<a name="line.307"></a>
<FONT color="green">308</FONT>          }<a name="line.308"></a>
<FONT color="green">309</FONT>          <a name="line.309"></a>
<FONT color="green">310</FONT>          if (valid) {<a name="line.310"></a>
<FONT color="green">311</FONT>            cResult.add(item);<a name="line.311"></a>
<FONT color="green">312</FONT>          }<a name="line.312"></a>
<FONT color="green">313</FONT>          else {<a name="line.313"></a>
<FONT color="green">314</FONT>            count++;<a name="line.314"></a>
<FONT color="green">315</FONT>          }<a name="line.315"></a>
<FONT color="green">316</FONT>        }<a name="line.316"></a>
<FONT color="green">317</FONT>        <a name="line.317"></a>
<FONT color="green">318</FONT>        for (Organization item : this.organizationList) {<a name="line.318"></a>
<FONT color="green">319</FONT>          valid = true;<a name="line.319"></a>
<FONT color="green">320</FONT>          <a name="line.320"></a>
<FONT color="green">321</FONT>          valid = valid &amp; this.checkUniqueId(item.getContact(), idType.idResearcher);<a name="line.321"></a>
<FONT color="green">322</FONT>          <a name="line.322"></a>
<FONT color="green">323</FONT>          if (item.getAffiliatedResearchers() != null) {<a name="line.323"></a>
<FONT color="green">324</FONT>            for (String link : item.getAffiliatedResearchers().getAffiliatedResearcher()) {<a name="line.324"></a>
<FONT color="green">325</FONT>              boolean validLink = this.checkUniqueId(link, idType.idResearcher);<a name="line.325"></a>
<FONT color="green">326</FONT>              if (!validLink) {<a name="line.326"></a>
<FONT color="green">327</FONT>                outputInfo("Organization " + item.getName() + ": Invalid researcher: " + link);<a name="line.327"></a>
<FONT color="green">328</FONT>              }<a name="line.328"></a>
<FONT color="green">329</FONT>              valid = valid &amp; validLink;<a name="line.329"></a>
<FONT color="green">330</FONT>            }<a name="line.330"></a>
<FONT color="green">331</FONT>          }<a name="line.331"></a>
<FONT color="green">332</FONT>          <a name="line.332"></a>
<FONT color="green">333</FONT>          if (valid) {<a name="line.333"></a>
<FONT color="green">334</FONT>            oResult.add(item);<a name="line.334"></a>
<FONT color="green">335</FONT>          }<a name="line.335"></a>
<FONT color="green">336</FONT>          else {<a name="line.336"></a>
<FONT color="green">337</FONT>            count++;<a name="line.337"></a>
<FONT color="green">338</FONT>          }<a name="line.338"></a>
<FONT color="green">339</FONT>        }<a name="line.339"></a>
<FONT color="green">340</FONT>    <a name="line.340"></a>
<FONT color="green">341</FONT>        for (Researcher item : this.researcherList) {<a name="line.341"></a>
<FONT color="green">342</FONT>          valid = true;<a name="line.342"></a>
<FONT color="green">343</FONT>          <a name="line.343"></a>
<FONT color="green">344</FONT>          valid = valid &amp; this.checkUniqueId(item.getOrganization(), idType.idOrganization);<a name="line.344"></a>
<FONT color="green">345</FONT>          <a name="line.345"></a>
<FONT color="green">346</FONT>          if (valid) {<a name="line.346"></a>
<FONT color="green">347</FONT>            rResult.add(item);<a name="line.347"></a>
<FONT color="green">348</FONT>          }<a name="line.348"></a>
<FONT color="green">349</FONT>          else {<a name="line.349"></a>
<FONT color="green">350</FONT>            outputInfo("Researcher " + item.getName() + ": Invalid organization: " <a name="line.350"></a>
<FONT color="green">351</FONT>                + item.getOrganization());<a name="line.351"></a>
<FONT color="green">352</FONT>            count++;<a name="line.352"></a>
<FONT color="green">353</FONT>          }<a name="line.353"></a>
<FONT color="green">354</FONT>        }<a name="line.354"></a>
<FONT color="green">355</FONT>    <a name="line.355"></a>
<FONT color="green">356</FONT>        if (!verboseMode) {<a name="line.356"></a>
<FONT color="green">357</FONT>          collaborationList = cResult;<a name="line.357"></a>
<FONT color="green">358</FONT>          organizationList = oResult;<a name="line.358"></a>
<FONT color="green">359</FONT>          researcherList = rResult;<a name="line.359"></a>
<FONT color="green">360</FONT>        }<a name="line.360"></a>
<FONT color="green">361</FONT>    <a name="line.361"></a>
<FONT color="green">362</FONT>        return count;<a name="line.362"></a>
<FONT color="green">363</FONT>      }<a name="line.363"></a>
<FONT color="green">364</FONT>      <a name="line.364"></a>
<FONT color="green">365</FONT>      /**<a name="line.365"></a>
<FONT color="green">366</FONT>       * Checks organizations list and removes invalid entries.<a name="line.366"></a>
<FONT color="green">367</FONT>       * <a name="line.367"></a>
<FONT color="green">368</FONT>       * @return Number of entries in all lists that failed semantic checks.<a name="line.368"></a>
<FONT color="green">369</FONT>       */<a name="line.369"></a>
<FONT color="green">370</FONT>      public int checkOrganizations() {<a name="line.370"></a>
<FONT color="green">371</FONT>        int count = 0;<a name="line.371"></a>
<FONT color="green">372</FONT>        <a name="line.372"></a>
<FONT color="green">373</FONT>        List&lt;Organization&gt; result = new ArrayList&lt;Organization&gt;();<a name="line.373"></a>
<FONT color="green">374</FONT>        <a name="line.374"></a>
<FONT color="green">375</FONT>        for (Organization item : this.organizationList) {<a name="line.375"></a>
<FONT color="green">376</FONT>          if (validOrganization(item)) {<a name="line.376"></a>
<FONT color="green">377</FONT>            item.setUniqueID(item.getName().replace(' ', '_'));<a name="line.377"></a>
<FONT color="green">378</FONT>            result.add(item);<a name="line.378"></a>
<FONT color="green">379</FONT>          }<a name="line.379"></a>
<FONT color="green">380</FONT>          else {<a name="line.380"></a>
<FONT color="green">381</FONT>            count++;<a name="line.381"></a>
<FONT color="green">382</FONT>          }<a name="line.382"></a>
<FONT color="green">383</FONT>        }<a name="line.383"></a>
<FONT color="green">384</FONT>        <a name="line.384"></a>
<FONT color="green">385</FONT>        if (!verboseMode) {<a name="line.385"></a>
<FONT color="green">386</FONT>          organizationList = result;<a name="line.386"></a>
<FONT color="green">387</FONT>        } <a name="line.387"></a>
<FONT color="green">388</FONT>        <a name="line.388"></a>
<FONT color="green">389</FONT>        return count;<a name="line.389"></a>
<FONT color="green">390</FONT>      }<a name="line.390"></a>
<FONT color="green">391</FONT>      <a name="line.391"></a>
<FONT color="green">392</FONT>      /**<a name="line.392"></a>
<FONT color="green">393</FONT>       * Checks collaborations list and removes invalid entries.<a name="line.393"></a>
<FONT color="green">394</FONT>       * <a name="line.394"></a>
<FONT color="green">395</FONT>       * @return Number of entries in all lists that failed semantic checks.<a name="line.395"></a>
<FONT color="green">396</FONT>       */<a name="line.396"></a>
<FONT color="green">397</FONT>      public int checkCollaborations() {<a name="line.397"></a>
<FONT color="green">398</FONT>        int count = 0;<a name="line.398"></a>
<FONT color="green">399</FONT>        <a name="line.399"></a>
<FONT color="green">400</FONT>        List&lt;Collaboration&gt; result = new ArrayList&lt;Collaboration&gt;();<a name="line.400"></a>
<FONT color="green">401</FONT>        <a name="line.401"></a>
<FONT color="green">402</FONT>        for (Collaboration item : this.collaborationList) {<a name="line.402"></a>
<FONT color="green">403</FONT>          if (validCollaboration(item)) {<a name="line.403"></a>
<FONT color="green">404</FONT>            item.setUniqueID(item.getName().replace(' ', '_'));<a name="line.404"></a>
<FONT color="green">405</FONT>            result.add(item);<a name="line.405"></a>
<FONT color="green">406</FONT>          }<a name="line.406"></a>
<FONT color="green">407</FONT>          else {<a name="line.407"></a>
<FONT color="green">408</FONT>            count++;<a name="line.408"></a>
<FONT color="green">409</FONT>          }<a name="line.409"></a>
<FONT color="green">410</FONT>        }<a name="line.410"></a>
<FONT color="green">411</FONT>        <a name="line.411"></a>
<FONT color="green">412</FONT>        if (!this.verboseMode) {<a name="line.412"></a>
<FONT color="green">413</FONT>          collaborationList = result;<a name="line.413"></a>
<FONT color="green">414</FONT>        }<a name="line.414"></a>
<FONT color="green">415</FONT>        <a name="line.415"></a>
<FONT color="green">416</FONT>        return count;<a name="line.416"></a>
<FONT color="green">417</FONT>      }<a name="line.417"></a>
<FONT color="green">418</FONT>      <a name="line.418"></a>
<FONT color="green">419</FONT>      /**<a name="line.419"></a>
<FONT color="green">420</FONT>       * Gets a list of semantic errors found from last check.<a name="line.420"></a>
<FONT color="green">421</FONT>       * <a name="line.421"></a>
<FONT color="green">422</FONT>       * @return List of strings.<a name="line.422"></a>
<FONT color="green">423</FONT>       */<a name="line.423"></a>
<FONT color="green">424</FONT>      public List&lt;String&gt; getErrorList() {<a name="line.424"></a>
<FONT color="green">425</FONT>        return this.errorList;<a name="line.425"></a>
<FONT color="green">426</FONT>      }<a name="line.426"></a>
<FONT color="green">427</FONT>      <a name="line.427"></a>
<FONT color="green">428</FONT>      /**<a name="line.428"></a>
<FONT color="green">429</FONT>       * Checks all lists, updates them, and removes invalid entries.<a name="line.429"></a>
<FONT color="green">430</FONT>       * <a name="line.430"></a>
<FONT color="green">431</FONT>       * @return Number of entries in all lists that failed semantic checks.<a name="line.431"></a>
<FONT color="green">432</FONT>       */<a name="line.432"></a>
<FONT color="green">433</FONT>      public int checkAll() {<a name="line.433"></a>
<FONT color="green">434</FONT>        errorList.clear();<a name="line.434"></a>
<FONT color="green">435</FONT>        <a name="line.435"></a>
<FONT color="green">436</FONT>        int count = 0;<a name="line.436"></a>
<FONT color="green">437</FONT>        <a name="line.437"></a>
<FONT color="green">438</FONT>        count += checkResearchers();<a name="line.438"></a>
<FONT color="green">439</FONT>        count += checkOrganizations();<a name="line.439"></a>
<FONT color="green">440</FONT>        count += checkCollaborations();    <a name="line.440"></a>
<FONT color="green">441</FONT>        <a name="line.441"></a>
<FONT color="green">442</FONT>        count += checkLinks();<a name="line.442"></a>
<FONT color="green">443</FONT>        <a name="line.443"></a>
<FONT color="green">444</FONT>    //    List&lt;String&gt; result = new ArrayList&lt;String&gt;();<a name="line.444"></a>
<FONT color="green">445</FONT>    //    result.addAll(errorList);<a name="line.445"></a>
<FONT color="green">446</FONT>        <a name="line.446"></a>
<FONT color="green">447</FONT>    //    return result;<a name="line.447"></a>
<FONT color="green">448</FONT>        return count;<a name="line.448"></a>
<FONT color="green">449</FONT>      }<a name="line.449"></a>
<FONT color="green">450</FONT>    }<a name="line.450"></a>




























































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